Free-living amoebae in an oil refinery wastewater treatment facility

Free Living Amoebae (FLA) are ubiquitous microorganisms reported from harsh environmental conditions. Oil refinery facilities consume vast volumes of water during their processes, generating a large amount of wastewater. The present study aimed to evaluate the wastewater treatment process in an oil refinery wastewater treatment facility (ORWWTF) for the presence of FLA. Water samples were collected from an oil refinery wastewater (ORWW) for nine months. After recording physical-chemical features, samples were cultivated onto non-nutrient agar (NNA). The discriminative fragments of the ribosomal RNA (rRNA) gene were amplified and sequenced to characterize the isolated FLA. Phylogenetic tree, and network analysis were employed to evaluate genetic relationships. The thermo- and osmotolerant tests were performed on the isolated FLA. Twenty-five (32.9%) samples were positive for FLA cultivation. Acanthamoeba spp., Vahlkampfiids, and Vermamoeba spp. were detected, of which Acanthamoeba species were predominant. There was no statistical correlation between pH, NH₃, PO₄, H₂S, and TDS with the presence of FLA. A statistical correlation between the presence of FLA and the type of wastewater treatment plants (WWTPs) was significant (P-value = 0.011). All Acanthamoeba spp. isolates belonged to the genotypes T4 (17/21; 80.95%) and T11 (4/21; 19.05%). Vahlkampfiids were Naegleria spp., (7/10; 70%), Tetramitus aberdonicus (1/10; 10%), Learamoeba spp., (1/10; 10%), and Vahlkampfia spp., (1/10; 10%). All three Vermamoeba spp. were V. vermiformis. The ORWW contains toxic materials, and a few microorganisms can stay active in these environments. This is the first study which isolates FLA from such super harsh conditions. For the first time, T. aberdonicus, and Learamoeba spp., were isolated from oily wastewater. Our findings signify the concern due to the distribution of potentially pathogenic FLA to downstream lands via treated wastewater that may be released after treatment processing.

Performance of machine learning techniques on prediction of esophageal varices grades among patients with cirrhosis

OBJECTIVES

All patients with cirrhosis should be periodically examined for esophageal varices (EV), however, a large percentage of patients undergoing screening, do not have EV or have only mild EV and do not have high-risk characteristics. Therefore, developing a non-invasive method to predict the occurrence of EV in patients with liver cirrhosis as a non-invasive method with high accuracy seems useful. In the present research, we compared the performance of several machine learning (ML) methods to predict EV on laboratory and clinical data to choose the best model.

METHODS

Four-hundred-and-ninety data from the Liver and Gastroenterology Research Center of Shahid Beheshti University of Medical Sciences in the period 2014-2021, were analyzed applying models including random forest (RF), artificial neural network (ANN), support vector machine (SVM), and logistic regression.

RESULTS

RF and SVM had the best results in general for all grades of EV. RF showed remarkably better results and the highest area under the curve (AUC). After that, SVM and ANN had the AUC of 98%, for grade 3, the SVM algorithm had the highest AUC after RF (89%).

CONCLUSIONS

The findings may help to better predict EV with high precision and accuracy and also can help reduce the burden of frequent visits to endoscopic centers. It can also help practitioners to manage cirrhosis by predicting EV with lower costs.

Low volume polyethylene glycol combined with senna versus high volume polyethylene glycol, which regimen is better for bowel preparation for colonoscopy? A randomized, controlled, and single‐blinded trial

Background and Aims

Bowel preparation affects the quality of colonoscopy. Reaching the optimal preparation has been a challenge for years. Polyethylene glycol (PEG) is the sole FDA‐approved substance for this purpose. However, patients find it unpleasant and often complain about its adverse effects. In this study, we aimed to reduce these complaints by lowering the amount of PEG and adding senna which is an herbal stimulant laxative.

Methods

Four hundred and eighty‐six patients were admitted for colonoscopy. Finally, 382 patients were enrolled in the study and we divided them into two groups; 186 patients were placed in which conventional high volume PEG‐alone regimen was consumed and 196 patients in which low volume PEG plus senna regimen was offered. The quality of colon preparation was compared between the two groups by independent two samples t‐test (or its corresponding nonparametric test), Fisher's exact, or χ² test in SPSS software version 22.

Results

The colon preparation quality was equally efficient in the two groups as 69.36% in the high volume PEG group and 71.94% in PEG plus senna group had adequate bowel preparation (p = 0.58). Adverse effects, like nausea, bloating, headache, and sleeplessness were significantly less in the low volume PEG plus senna group.

Conclusion

Besides the fact that bowel preparation by low volume PEG plus senna combination was noninferior to the conventional high volume PEG‐alone regimen, the side effects were much less common with the low volume PEG plus senna regimen.

Application of recombinant antibodies for treatment of Clostridioides difficile infection: Current status and future perspective

Clostridioides difficile (C. difficile), known as the major cause of antibiotic-associated diarrhea, is regarded as one of the most common healthcare-associated bacterial infections worldwide. Due to the emergence of hypervirulent strains, development of new therapeutic methods for C. difficile infection (CDI) has become crucially important. In this context, antibodies have been introduced as valuable tools in the research and clinical environments, as far as the effectiveness of antibody therapy for CDI was reported in several clinical investigations. Hence, production of high-performance antibodies for treatment of CDI would be precious. Traditional approaches of antibody generation are based on hybridoma technology. Today, application of in vitro technologies for generating recombinant antibodies, like phage display, is considered as an appropriate alternative to hybridoma technology. These techniques can circumvent the limitations of the immune system and they can be exploited for production of antibodies against different types of biomolecules in particular active toxins. Additionally, DNA encoding antibodies is directly accessible in in vitro technologies, which enables the application of antibody engineering in order to increase their sensitivity and specificity. Here, we review the application of antibodies for CDI treatment with an emphasis on recombinant fragment antibodies. Also, this review highlights the current and future prospects of the aforementioned approaches for antibody-mediated therapy of CDI.

The double-edged sword of probiotic supplementation on gut microbiota structure in Helicobacter pylori management

As Helicobacter pylori management has become more challenging and less efficient over the last decade, the interest in innovative interventions is growing by the day. Probiotic co-supplementation to antibiotic therapies is reported in several studies, presenting a moderate reduction in drug-related side effects and a promotion in positive treatment outcomes. However, the significance of gut microbiota involvement in the competence of probiotic co-supplementation is emphasized by a few researchers, indicating the alteration in the host gastrointestinal microbiota following probiotic and drug uptake. Due to the lack of long-term follow-up studies to determine the efficiency of probiotic intervention in H. pylori eradication, and the delicate interaction of the gut microbiota with the host wellness, this review aims to discuss the gut microbiota alteration by probiotic co-supplementation in H. pylori management to predict the comprehensive effectiveness of probiotic oral administration.Abbreviations: acyl-CoA- acyl-coenzyme A; AMP- antimicrobial peptide; AMPK- AMP-activated protein kinase; AP-1- activator protein 1; BA- bile acid; BAR- bile acid receptor; BCAA- branched-chain amino acid; C2- acetate; C3- propionate; C4- butyrate; C5- valeric acid; CagA- Cytotoxin-associated gene A; cAMP- cyclic adenosine monophosphate; CD- Crohn's disease; CDI- C. difficile infection; COX-2- cyclooxygenase-2; DC- dendritic cell; EMT- epithelial-mesenchymal transition; FMO- flavin monooxygenases; FXR- farnesoid X receptor; GPBAR1- G-protein-coupled bile acid receptor 1; GPR4- G protein-coupled receptor 4; H2O2- hydrogen peroxide; HCC- hepatocellular carcinoma; HSC- hepatic stellate cell; IBD- inflammatory bowel disease; IBS- irritable bowel syndrome; IFN-γ- interferon-gamma; IgA immunoglobulin A; IL- interleukin; iNOS- induced nitric oxide synthase; JAK1- janus kinase 1; JAM-A- junctional adhesion molecule A; LAB- lactic acid bacteria; LPS- lipopolysaccharide; MALT- mucosa-associated lymphoid tissue; MAMP- microbe-associated molecular pattern; MCP-1- monocyte chemoattractant protein-1; MDR- multiple drug resistance; mTOR- mammalian target of rapamycin; MUC- mucin; NAFLD- nonalcoholic fatty liver disease; NF-κB- nuclear factor kappa B; NK- natural killer; NLRP3- NLR family pyrin domain containing 3; NOC- N-nitroso compounds; NOD- nucleotide-binding oligomerization domain; PICRUSt- phylogenetic investigation of communities by reconstruction of unobserved states; PRR- pattern recognition receptor; RA- retinoic acid; RNS- reactive nitrogen species; ROS- reactive oxygen species; rRNA- ribosomal RNA; SCFA- short-chain fatty acids; SDR- single drug resistance; SIgA- secretory immunoglobulin A; STAT3- signal transducer and activator of transcription 3; T1D- type 1 diabetes; T2D- type 2 diabetes; Th17- T helper 17; TLR- toll-like receptor; TMAO- trimethylamine N-oxide; TML- trimethyllysine; TNF-α- tumor necrosis factor-alpha; Tr1- type 1 regulatory T cell; Treg- regulatory T cell; UC- ulcerative colitis; VacA- Vacuolating toxin A.

The interplay between Helicobacter pylori and the gut microbiota: An emerging driver influencing the immune system homeostasis and gastric carcinogenesis

The human gut microbiota are critical for preserving the health status because they are required for digestion and nutrient acquisition, the development of the immune system, and energy metabolism. The gut microbial composition is greatly influenced by the colonization of the recalcitrant pathogen Helicobacter pylori (H. pylori) and the conventional antibiotic regimens that follow. H. pylori is considered to be the main microorganism in gastric carcinogenesis, and it appears to be required for the early stages of the process. However, a non-H. pylori microbiota profile is also suggested, primarily in the later stages of tumorigenesis. On the other hand, specific groups of gut microbes may produce beneficial byproducts such as short-chain fatty acids (acetate, butyrate, and propionate) that can modulate inflammation and tumorigenesis pathways. In this review, we aim to present how H. pylori influences the population of the gut microbiota to modify the host immunity and trigger the development of gastric carcinogenesis. We will also highlight the effect of the gut microbiota on immunotherapeutic approaches such as immune checkpoint blockade in cancer treatment to present a perspective for further development of innovative therapeutic paradigms to prevent the progression of H. pylori-induced stomach cancer.

Combination of pioglitazone and dendritic cell to optimize efficacy of immune cell therapy in CT26 tumor models

Introduction

The maturation faith of dendritic cells is restrained by the inflammatory environment and cytokines, such as interleukin-6 and its downstream component. Therefore, introducing the suitable antigen to dendritic cells is crucial. However, reducing the severity of the suppressive tumor microenvironment is indispensable. The present study examined the combination therapy of lymphocyte antigen 6 family member E (LY6E) pulsed mature dendritic cells (LPMDCs) and pioglitazone against colorectal cancer (CRC) to elevate the effectiveness of cancer treatment through probable role of pioglitazone on inhibiting IL-6/STAT3 pathway.

Methods

Dendritic cells were generated from murine bone marrow and were pulsed with lymphocyte antigen 6 family member E peptide to assess antigen-specific T-cell proliferation and cytotoxicity assay with Annexin/PI. The effect of pioglitazone on interleukin (IL)-6/STAT3 was evaluated in vitro by real-time polymerase chain reaction (PCR). Afterward, the CRC model was established by subcutaneous injection of CT26, mouse colon carcinoma cell line, in female mice. After treatment, tumor, spleen, and lymph nodes samples were removed for histopathological, ELISA, and real-time PCR analysis.

Results

In vitro results revealed the potential of lysate-pulsed dendritic cells in the proliferation of double-positive CD3-8 splenocytes and inducing immunogenic cell death responses, whereas pioglitazone declined the expression of IL-6/STAT3 in colorectal cell lines. In animal models, the recipient of LPMDCs combined with pioglitazone demonstrated high tumor-infiltrating lymphocytes. Elevating the IL-12 and interferon-gamma (IFN-γ) levels and prolonged survival in lysate-pulsed dendritic cell and combination groups were observed.

Conclusion

Pioglitazone could efficiently ameliorate the immunosuppressive feature of the tumor microenvironment, mainly through IL-6. Accordingly, applying this drug combined with LPMDCs provoked substantial CD8 positive responses in tumor-challenged animal models.

Identifying novel host-based diagnostic biomarker panels for COVID-19: a whole-blood/nasopharyngeal transcriptome meta-analysis

BACKGROUND

Regardless of improvements in controlling the COVID-19 pandemic, the lack of comprehensive insight into SARS-COV-2 pathogenesis is still a sophisticated challenge. In order to deal with this challenge, we utilized advanced bioinformatics and machine learning algorithms to reveal more characteristics of SARS-COV-2 pathogenesis and introduce novel host response-based diagnostic biomarker panels.

METHODS

In the present study, eight published RNA-Seq datasets related to whole-blood (WB) and nasopharyngeal (NP) swab samples of patients with COVID-19, other viral and non-viral acute respiratory illnesses (ARIs), and healthy controls (HCs) were integrated. To define COVID-19 meta-signatures, Gene Ontology and pathway enrichment analyses were applied to compare COVID-19 with other similar diseases. Additionally, CIBERSORTx was executed in WB samples to detect the immune cell landscape. Furthermore, the optimum WB- and NP-based diagnostic biomarkers were identified via all the combinations of 3 to 9 selected features and the 2-phases machine learning (ML) method which implemented k-fold cross validation and independent test set validation.

RESULTS

The host gene meta-signatures obtained for SARS-COV-2 infection were different in the WB and NP samples. The gene ontology and enrichment results of the WB dataset represented the enhancement in inflammatory host response, cell cycle, and interferon signature in COVID-19 patients. Furthermore, NP samples of COVID-19 in comparison with HC and non-viral ARIs showed the significant upregulation of genes associated with cytokine production and defense response to the virus. In contrast, these pathways in COVID-19 compared to other viral ARIs were strikingly attenuated. Notably, immune cell proportions of WB samples altered in COVID-19 versus HC. Moreover, the optimum WB- and NP-based diagnostic panels after two phases of ML-based validation included 6 and 8 markers with an accuracy of 97% and 88%, respectively.

CONCLUSIONS

Based on the distinct gene expression profiles of WB and NP, our results indicated that SARS-COV-2 function is body-site-specific, although according to the common signature in WB and NP COVID-19 samples versus controls, this virus also induces a global and systematic host response to some extent. We also introduced and validated WB- and NP-based diagnostic biomarkers using ML methods which can be applied as a complementary tool to diagnose the COVID-19 infection from non-COVID cases.

Fenofibrate in primary sclerosing cholangitis; a randomized, double-blind, placebo-controlled trial

Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease with no medical treatment proven to improve survival and postpone liver transplantation. Previous studies have shown the effectiveness of fibrates in primary biliary cholangitis. The current study prospectively evaluated the effect of fenofibrate on PSC patients. We administered 200 mg of fenofibrate to PSC patients in the intervention arm and a placebo in the control arm once per day for 6 months and evaluated liver biochemistries (alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, bilirubin, and albumin) and the Mayo Risk Score at the start and end of the study. The primary endpoint was defined as a reduction greater than 50% or normalization of ALP levels. Secondary endpoints were an improvement in the Mayo Risk Score and serum bilirubin levels. Thirty patients were included (19 female, 11 male, 40.2 ± 9.2 years old), all under treatment with Ursodeoxycholic acid prior to this study. ALP and ALT levels significantly decreased in the fenofibrate group, by 64.7% (mean difference = 557, p = 0.004, 95% CI = 208.72, 905.27) and 52.78%, (p = 0.006), respectively. The primary endpoint was achieved in 66.7% of patients (10 in 15) in the fenofibrate group versus 20% of patients (3 in 15) in the placebo group (p = 0.009). Other endpoints were not met. As studies have demonstrated lower levels of ALP may improve outcomes for PSC, our study resulted in significantly lower levels of ALP in the fenofibrate group, which could translate into better disease prognosis in PSC.

Identifying predictors of varices grading in patients with cirrhosis using ensemble learning

Objectives

The present study was conducted to improve the performance of predictive methods by introducing the most important factors which have the highest effects on the prediction of esophageal varices (EV) grades among patients with cirrhosis.

Methods

In the present study, the ensemble learning methods, including Catboost and XGB classifier, were used to choose the most potent predictors of EV grades solely based on routine laboratory and clinical data, a dataset of 490 patients with cirrhosis gathered. To increase the validity of the results, a five-fold cross-validation method was applied. The model was conducted using python language, Anaconda open-source platform. TRIPOD checklist for prediction model development was completed.

Results

The Catboost model predicted all the targets correctly with 100% precision. However, the XGB classifier had the best performance for predicting grades 0 and 1, and totally the accuracy was 91.02%. The most significant variables, according to the best performing model, which was CatBoost, were child score, white blood cell (WBC), vitalism K (K), and international normalized ratio (INR).

Conclusions

Using machine learning models, especially ensemble learning models, can remarkably increase the prediction performance. The models allow practitioners to predict EV risk at any clinical visit and decrease unneeded esophagogastroduodenoscopy (EGD) and consequently reduce morbidity, mortality, and cost of the long-term follow-ups for patients with cirrhosis.

Gene expression analysis of intestinal IL-8, IL-17 A and IL-10 in patients with celiac and inflammatory bowel diseases

BACKGROUND

Celiac disease (CeD) and inflammatory bowel disease (IBD) are accompanied by impaired immune responses. To study the immune regulation of these diseases, we evaluated the expression levels of pro-inflammatory (IL-8 and IL-17 A) and anti-inflammatory (IL-10) cytokines in intestinal biopsy specimens of CeD and IBD patients in comparison to healthy subjects.

METHODS AND RESULTS

Intestinal biopsies were collected from 33 patients with IBD, 47 patients with CeD, and 20 healthy individuals. Total RNA was extracted and mRNA expression levels of IL-8, IL-17 A and IL-10 were assessed by qPCR. P-value < 0.05 was considered statistically significant. The expression levels of IL-8 and IL-17 A were higher in biopsies of IBD (UC and CD) and CeD patients compared to the control group (P < 0.05). IBD patients (UC and CD) had higher IL-8 intestinal level than CeD patients (P < 0.0001 and P = 0.0007, respectively). The expression of IL-10 was significantly down-regulated in intestinal biopsies of CeD and IBD patients compared with controls (P < 0.001). In addition, the expression level of this cytokine was significantly lower in IBD patients (P < 0.001 for UC patients and P < 0.0001 for CD patients) than CeD group.

CONCLUSIONS

The three selected pro- and anti-inflammatory cytokines showed a similar expression pattern in both IBD and CeD patients. As IBD and CeD are immune-mediated disorders and are accompanied by inflammatory events, the understanding of the similarities and differences among them can help researchers to find out useful candidate therapeutic protocols. We suggest that larger cohort studies be organized to achieve more insights into this regulation.

Detection of SARS-CoV-2 Genome in Stool and Plasma Samples of Laboratory Confirmed Iranian COVID-19 Patients

Coronavirus disease 2019 (COVID19), caused by the severe acute respiratory syndrome coronavirus 2 (SARSCoV2), was first discovered in China in late 2019 and quickly spread worldwide. Although nasopharyngeal swab sampling is still the most popular approach identify SARS-CoV-2 carriers, other body samples may reveal the virus genome, indicating the potential for virus transmission via non-respiratory samples. In this study, researchers looked at the presence and degree of SARS-CoV-2 genome in stool and plasma samples from 191 Iranian COVID-19 patients, and looked for a link between these results and the severity of their disease. SARS-CoV-2 RNA shedding in feces and plasma of COVID-19 patients was assessed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Medical data were collected and evaluated, including Clinical features, demographics, radiological, and laboratory findings of the patients. Plasma samples from 117 confirmed laboratory patients were evaluated and 24 out of 117 patients (20.51%) tested positive for SARS-COV-2 RNA. Besides, 20 out of 74 patients (27.03%) tested positive for SARS-COV-2 RNA in stool samples. There seems to be no relationship between the presence of SARS-CoV-2 genome in fecal and plasma samples of Covid-19 patients and the severity of illness. We provide evidence of the SARS-CoV-2 genome presence in stool and plasma samples of Iranian COVID-19 patients.

The Potential Use of Antibiotics Against Helicobacter pylori Infection: Biopharmaceutical Implications

Helicobacter pylori (H. pylori) is a notorious, recalcitrant and silent germ, which can cause a variety of debilitating stomach diseases, including gastric and duodenal ulcers and gastric cancer. This microbe predominantly colonizes the mucosal layer of the human stomach and survives in the inhospitable gastric microenvironment, by adapting to this hostile milieu. In this review, we first discuss H. pylori colonization and invasion. Thereafter, we provide a survey of current curative options based on polypharmacy, looking at pharmacokinetics, pharmacodynamics and pharmaceutical microbiology concepts, in the battle against H. pylori infection.

Expression of Toll-Like Receptors 2, 4 and 5 in Relation to Gut Microbiota in Colon Neoplasm Patients with and without Inflammatory Bowel Disease

Background:

Toll-Like Receptors (TLRs) are the critical mediators of inflammatory routs in the gut, which play an essential role in regulating the immune responses towards various ligands derived from pathogenic bacteria. Also, TLR signaling has been implicated in the development of Inflammatory Bowel Disease (IBD), Adenomatous Polyp (AP), and Colorectal Cancer (CRC). Here, we aimed to examine the expression of some TLRs concerning certain fecal bacteria in AP and CRC patients with and without IBD.

Methods:

This case-control study collected fecal and colonic tissue samples from 93 patients versus Normal Controls (NC) via colonoscopy. Fecal samples were used for DNA extraction, and the abundance of selected fecal bacteria was determined by absolute real-time PCR. Also, the gene expression of TLR2, 4, and 5 was analyzed using RT-PCR on the colonic tissues of participants.

Results:

Compared to NC individuals, in AP and CRC patients, the mRNA expressions of TLR4 and TLR2 were significantly increased while TLR5 was decreased. A meaningful association between TLRs mRNA expression levels and the abundance of some selected fecal bacteria was detected. Also, there was a significant relationship between participant’s food regimes, smoking habit and intestinal TLRs expression.

Conclusion:

Our study proposed the important role of TLRs during adenomatous and CRC formation. Alterations in TLRs expression associated with certain gut bacteria may contribute to disease development.

Detection and quantification of Epstein-Barr virus, cytomegalovirus, and human herpesvirus-6 in stomach frozen tissue of chronic gastritis and gastric cancer patients

Human herpes viruses (HHVs) are among the most common infectious agents detected in the gastrointestinal tract that might be involved in oncogenesis and other gastrointestinal disorders. Although the link between the Epstein-Barr virus (EBV) and gastric cancer (GC) has been established, the role of the viruses in various stomach diseases remains unknown. The frequencies and viral copy number of EBV, cytomegalovirus (CMV), and human herpesvirus 6 (HHV-6) among 50 gastric cancer tumors and 105 chronic gastritis tissues were measured by quantitative real-time PCR. In the tumor specimens and the adjacent normal tissues EBV was found in 60% and 30.9%, CMV in 14% and 4.7%, and HHV-6 in 18%, and 14.2%, respectively. The detection rate of EBV and CMV was found to be significantly higher in tumor tissues relative to the adjacent normal tissues. Also, in chronic gastritis, the frequency of EBV, CMV, and HHV-6 was 19%, 12.3%, and 15.2%, respectively, compared with 16.4%, 1.1%, and 8.2% in their corresponding normal tissues. Here, the CMV frequency was found to be significantly higher in gastritis tissues relative to the adjacent normal tissues. Furthermore, viral load in both gastric cancer and gastritis groups was higher in either tumor or gastritis lesion compared with matched adjacent normal tissue. This study showed a clear association between gastric cancer with both EBV and CMV. Meanwhile, analyses revealed a strong association between the EBV, CMV, and HHV-6 viral loads with gastritis (P = 0.0026, P < 0.0001, and P = 0.0405, respectively). Our results suggest that these three viruses might contribute to the induction and development the gastritis and gastric cancer.

Molecular Identification, Subtypes Distribution, and Alleles Discrimination of Blastocystis sp., Isolated from Immunocompromised Subjects in Iran

Background:

Blastocystis sp., is a prevalent protist isolated from humans and animals, which its opportunistic role in immunocompromised patients is still controversial. The current study aimed to evaluate the subtype and alleles distribution of Blastocystis sp., among immunocompromised patients.

Methods:

Totally, 33 microscopically Blastocystis-positive stool samples, isolated from Guilan province during April 2018 to May 2019 were investigated. Total DNA extraction was performed and the barcoding region of the small subunit ribosomal RNA (SSU rRNA) gene was amplified. Targeted fragments were sequenced to characterize subtypes and relevant alleles. Phylogenetic tree was constructed using Maximum-likelihood and Tamura 3-parameter to illustrate the correlation between subtypes and certain immunodeficiency.

Results:

Subtype analysis revealed the presence of ST1, ST2, ST3, and ST7 among 13/33 (39.4%), 5 (15.2%), 14/33 (42.4%), and 1/33 (3%), of samples, respectively. ST1 was the major subtype among cancer patients 5/7 (71.42%), while ST3 was the predominant subtype among rheumatoid arthritis (RA) patients 3/6 (50%), internal ward patients 5/10 (50%), and asthma and allergy patients 2/3 (66.66%). ST7 was isolated from a patient hospitalized in internal ward. No significant correlation was seen between the type of immunodeficiency and subtypes (P-value = 0.771). The phylogenetic tree showed no separation regarding the type of immunodeficiency.

Conclusion:

Among studied immunocompromised patients, ST3 was the most prevalent subtype followed by ST1. There was no specific correlation between subtypes and alleles with type of immunodeficiency. Putative zoonotic alleles were highlighted the probability of zoonotic transmission for Blastocystis sp.

Machine learning-based system for prediction of ascites grades in patients with liver cirrhosis using laboratory and clinical data: design and implementation study

OBJECTIVES

The aim of the study was to implement a non-invasive model to predict ascites grades among patients with cirrhosis.

METHODS

In the present study, we used modern machine learning (ML) methods to develop a scoring system solely based on routine laboratory and clinical data to help physicians accurately diagnose and predict different degrees of ascites. We used ANACONDA3-5.2.0 64 bit, free and open-source platform distribution of Python programming language with numerous modules, packages, and rich libraries that provide various methods for classification problems. Through the 10-fold cross-validation, we employed three common learning models on our dataset, k-nearest neighbors (KNN), support vector machine (SVM), and neural network classification algorithms.

RESULTS

According to the data received from the research institute, three types of data analysis have been performed. The algorithms used to predict ascites were KNN, cross-validation (CV), and multilayer perceptron neural networks (MLPNN), which achieved an average accuracy of 94, 91, and 90%, respectively. Also, in the average accuracy of the algorithms, KNN had the highest accuracy of 94%.

CONCLUSIONS

We applied well-known ML approaches to predict ascites. The findings showed a strong performance compared to the classical statistical approaches. This ML-based approach can help to avoid unnecessary risks and costs for patients with acute stages of the disease.

Overview of Three Proliferation Pathways (Wnt, Notch, and Hippo) in Intestine and Immune System and Their Role in Inflammatory Bowel Diseases (IBDs)

Inflammatory bowel disease (IBD) is a disorder, which involves the gastrointestinal (GI) tract consisting Crohn's disease (CD) and ulcerative colitis (UC). The etiology of this disease is not yet clear and, hence, there are numerous medications and treatments for patients with IBD, although a definite and permanent treatment is still missing. Therefore, finding novel therapeutic approaches are vital for curing patients with IBD. In the GI tract, there are various lineages of cells with different roles that their existence is necessary for the barrier function of intestinal epithelial cells (IECs). Therefore, signaling pathways, which manage the hemostasis of cell lineages in intestine, such as Wnt, Notch, and Hippo, could have crucial roles in regulation of barrier function in the intestine. Additionally, these signaling pathways function as a governor of cell growth, tissue homeostasis, and organ size. In patients with IBD, recent studies have revealed that these signaling pathways are dysregulated that it could result in depletion or excess of a cell lineage in the intestine. Moreover, dysregulation of these signaling pathways in different cell lineages of the immune system could lead to dysregulation of the immune system's responses in IBD. In this article, we summarized the components and signaling of Wnt, Notch, and Hippo pathways and their role in the intestine and immune system. Furthermore, we reviewed latest scientific literature on the crosstalk among these three signaling pathways in IBD. An overview of these three signaling pathways and their interactions in IBD could provide a novel insight for prospective study directions into finding efficient medications or treatments.

Gold-based nanoplatform for a rapid lateral flow immunochromatographic test assay for gluten detection

Background

Gluten, a food allergen, is available in foods derived from wheat, rye and barley. It damages the small intestine and causes celiac disease. Herein, we designed a rapid immunochromatographic lateral flow test assay for detecting the gluten contents of raw materials. In this rapid test, the presence of gluten was screened through the capturing of gliadin (a toxic component of gluten) by two identical gliadin monoclonal antibodies. One of the antibodies was immobilized on the membrane in the test zone as a capture reagent. The other antibody was labeled with gold nanoparticles (AuNPs) as a detector reagent.

Results

Gold nanoparticles with a size of about 20 nm were synthesized and conjugated to the gliadin monoclonal antibodies. The detection limit of the experimental assay was 20 ppm and positive results were visualized after 15 min using only 40 μL of the extracted sample for each test. Analysis of different flour samples identified the best sensitivity and specificity of the lateral flow test strip (LFTS).

Conclusion

The experimental LFTS is an easy-to-use and rapid method for the screening of gluten level in raw materials. The LFTS may be employed to ensure the safety of foods.

Formulation of Neem oil-loaded solid lipid nanoparticles and evaluation of its anti-Toxoplasma activity

BACKGROUND

Toxoplasmosis is caused by an intracellular zoonotic protozoan, Toxoplasma gondii, which could be lethal in immunocompromised patients. This study aimed to synthesize Neem oil-loaded solid lipid nanoparticles (NeO-SLNs) and to evaluate the anti-Toxoplasma activity of this component.

METHODS

The NeO-SLNs were constructed using double emulsification method, and their shape and size distribution were evaluated using transmission electron microscope (TEM) and dynamic light scattering (DLS), respectively. An MTT assay was employed to evaluate the cell toxicity of the component. The anti-Toxoplasma activity of NeO-SLNs was investigated using vital (trypan-blue) staining. Anti-intracellular Toxoplasma activity of NeO-SLNs was evaluated in T. gondii-infected Vero cells.

RESULTS

The TEM analysis represented round shape NeO-SLNs with clear and stable margins. DLS analysis showed a mean particle size 337.6 nm for SLNs, and most of nanoparticles were in range 30 to 120 nm. The cell toxicity of NeO-SLNs was directly correlated with the concentration of the component (P-value = 0.0013). The concentration of NeO-SLNs, which was toxic for at least 50% of alive T. gondii (cytotoxic concentration (CC50)), was > 10 mg/mL. The ability of NeO-SLNs to kill Toxoplasma was concentration-dependent (P-value < 0.0001), and all concentrations killed at least 70% of alive tachyzoites. Furthermore, the viability of T. gondii- infected Vero cells was inversely correlated with NeO-SLNs concentrations (P-value = 0.0317), and in the concentration 100 μg/mL at least 75% of T. gondii- infected Vero cells remained alive.

CONCLUSIONS

Overall, our findings demonstrated that the NeO-SLNs was able to kill T. gondii tachyzoites in concentration 100 μg/mL with a cell toxicity lower than 20%. Such results suggest that employing SLNs as carrier for NeO can effectively kill T. gondii tachyzoites with acceptable cell toxicity. Our findings also showed that SLNs capsulation of the NeO can lead to prolonged release of the extract, suggesting that NeO-SLNs could be also employed to clear cyst stages, which should be further investigated in animal models.

Modulation of microRNAs and claudin-7 in Caco-2 cell line treated with Blastocystis sp., subtype 3 soluble total antigen

Background

Blastocystis sp., is a eukaryote of the large intestine, which is reported from almost all countries. The pathogenesis of this protist is not clear. The current study aimed to analyze the effects of Blastocystis sp., ST3 soluble total antigen (B3STA) on the microRNAs (miRNAs) involved in the gut permeability and also pro-inflammatory cytokines, occludin, and claudin-7.

Methods

Blastocystis sp., ST3 isolated from stool sample was purified, and its soluble total antigen was extracted using freeze and thawing. The Caco-2 cell line was treated with B3STA for 24 h and the expression levels of mir-16, mir-21, mir-29a, mir-223, and mir-874 were analyzed. In addition, the expression levels of il-8, il-15, occludin, and claudin-7 genes were assessed.

Results

B3STA significantly upregulated the expression of mir-223, and mir-874, and downregulated mir-29a. The expression of mir-16 and mir-21 was not significant. In addition, the expression of il-8 and il-15 was not significant. B3STA significantly decreased the expression level of claudin-7 (P-value < 0.0001), but the expression of occludin was not significant. Our results showed significant correlation between all studied miRNAs, except mir-29a, with downregulation of claudin-7.

Conclusions

This is the first study investigating the effects of Blastocystis sp., ST3 isolated from symptomatic subjects on the expression levels of miRNAs involved in the gut permeability. Our results demonstrated that B3STA may change miRNA expression, which are involved in the gut barrier integrity, and downregulates claudin-7, which is known as sealing factor.

Cost-effectiveness analysis of infliximab versus CinnoRA in the treatment of moderate to severe ulcerative colitis in Iranian patients

Introduction: As two biological agents, infliximab (IFX) and biosimilar adalimumab (CinnoRA®) are routinely used in the clinical management of ulcerative colitis (UC) in Iran. Objectives: This study was done to evaluate the cost-effectiveness of IFX versus CinnoRA for the treatment of moderate-to-severe UC patients. Patients and Methods: To accomplish this, we developed a hybrid decision-tree/microsimulation (MS) approach for modeling UC’s natural history. We populated our model with available data on probabilities, costs, utilities / disutilities, and emergent adverse effects. Costs were reported in Iranian Rial (IRR) and in April 2021 US dollars ($). One-way and multiple sensitivity analyses were used to determine the uncertainty of the model’s parameters. Results: For five, 10, and lifetime horizon times, patients on IFX received slightly more quality-adjusted life-year (QALY) per year in remission and experienced about 3 to 5 times less surgery than CinnoRA patients. With willingness-to-pay (WTP) thresholds of 1800 ($7826.08), 820($3565.21), and 520 ($2260.86) million IRR for these horizon times, IFX was cost-effective with 100% certainty. Our findings were highly sensitive to the number of adverse effects. Conclusion: Our results demonstrated that IFX is more effective and more costly than CinnoRA, and if we ignore the predicted surgeries, CinnoRA is nearly as effective as IFX. However, these findings should be cautiously interpreted without a robust clinical trial of CinnoRA in UC patients. Since the impact of CinnoRA may have been over/underestimated.

A systematic review and meta-analysis on the co-infection of Helicobacter pylori with intestinal parasites: public health issue or neglected correlation?

The current study was conducted to assess the prevalence and odds ratio (OR) of co-infection of Helicobacter pylori (H. pylori) and intestinal parasites (IPs). English databases were searched. A total of 18 studies including 14 studies with cross-sectional design (a total of 3739 participants) and 4 studies with case-control design (397 patients and 320 controls) met the eligibility criteria. The pooled prevalence of H. pylori, intestinal parasite infections (IPIs), and their co-infections in different populations were 48.3% (95% CI, 34.1-62.8%), 15.4% (95% CI, 10-22.8%), and 11% (95% CI, 6.7-17.6%), respectively. The co-infection of H. pylori and Giardia was 7.6% (95% CI, 4.9-11.7%). Although statistically not significant, the risk of co-infection of H. pylori and IPIs was higher in case group compared to control group (OR, 1.59; 95% CI, 0.77-3.25). The overlaps between H. pylori and IPIs in countries with lower human development index (HDI) and income levels were high.